For time immemorial, mankind has sourced surrounding organisms for therapeutic purposes, and most of the commercial antibiotics still have a natural origin. During the last 10 years, in an effort to rationalize and to speed up antibacterial discovery processes, the industry has moved from natural products and a molecule-oriented discovery strategy to synthetic molecules and a target-oriented strategy.
After years of uniformization of antibiotic R&D process, with an unprecedented high attrition rate, it is necessary to return to natural resources. Indeed, the screening of natural product libraries usually yields a higher percentage of antibiotics hits than that of chemical libraries, and consequently provides a higher probability to obtain a therapeutic. The first reason probably lies in the ecologic role of the antibiotics, which have been optimized through the course of evolution, to defend plants, animals and micro-organisms against other living organisms. Furthermore, natural products are generally as lipophilic as combinatorial compounds, but they have an unparalleled structural diversity and dispersion in chemical space. This helps to find rare hydrophilic hits which can be optimized for in vivo applications.
It is generally assumed that 20 to 30 percent of the bacteria isolated from environmental sources such as soil or water are antibiotics producers (Bérdy, 2005). For obvious reasons, the fitter and the most represented bacteria are the most frequently isolated. This explains why many antibiotics produced by Bacillus or Pseudomonas have already been documented, and why it is more and more difficult to find new molecular entities produced by these genera. Other families of under-represented bacteria, more adapted to antibiotic production, due to a bigger genome, can be easily isolated with adapted techniques. This is the case of actinomycetals, by far the best antibiotic producers (Bérdy, 2005). They were extensively studied by the pharmaceutical industry between 1950 and 1980, and it is now difficult to identify strains producing non-redundant molecules.
In the last decade, efforts have been devoted to isolating rare bacteria in order to find new chemical entities of pharmaceutical interest. Myxobacteria, for example, are known since the 1940's, but due to difficulties encountered for isolating them, they were under-represented in the collections. Thanks to an extensive collection campaign carried out by Reichenbach H and collaborators, so far about 80 different compounds and 450 structural variants produced by Myxobacteria have been characterized (Reichenbach, 2001). Many of those compounds were new. Among them is the antineoplasic drug, epothilones, currently being evaluated in clinical trials.
It is generally recognized, however, that microbiologists are unable to culture most soil microorganisms (Schoenborn et al., 2005). The number of cultivable cells in soil is often only about 1% of the total number of cells present. Most of these bacteria are difficult to detect and isolate using standard isolation techniques, either because they are rare in the environment, or because they are less adapted to environmental conditions than other bacteria like Pseudomonas spp. or Bacillus spp. and are rapidly overgrown. Several isolation techniques aiming to increase the diversity of the isolates have been published. For example, serial liquid dilution culture has been used successfully to improve cultivability (Schoenborn et al., 2005) and to facilitate the isolation of bacteria from diverse environments. Yang et al., 2008, also described the use of microwave treatment to isolate rare actinomycetes. WO02/059351 concerns a method for enriching a microbial population from a natural environment using e.g., hot spring water.
However, environmental microorganisms still represent a rich and unexploited resource of novel compounds and activities, and there is a need in the art for improved or alternative methods to identify bacteria of interest.